From 968810c3e0339a615a3d6f7793eaae29edd47106 Mon Sep 17 00:00:00 2001 From: james94 <james94@mi.fu-berlin.de> Date: Wed, 24 Aug 2022 09:31:54 +0200 Subject: [PATCH] fix conda --- Snakefile | 19 +++++++++---------- envs/AUXILIARY_PYTHON_SCRIPTS.yaml | 1 + envs/UNZIP_and_QC.yaml | 11 ++++++----- rules/evaluate.smk | 12 ++++++------ 4 files changed, 22 insertions(+), 21 deletions(-) diff --git a/Snakefile b/Snakefile index 8338c8b..0971ea7 100644 --- a/Snakefile +++ b/Snakefile @@ -18,9 +18,9 @@ with open(config['resources'], 'r') as f: resource = yaml.safe_load(f) ### GET BASENAME FOR READS WILDCARDS ### -def getBasename4Reads(path): - base=os.path.basename(path) - return os.path.splitext(base)[0] +# def getBasename4Reads(path): +# base=os.path.basename(path) +# return os.path.splitext(base)[0] ### CHECK IF INPUT IS GZIPPED ### def gzipped_or_not(path): @@ -41,14 +41,13 @@ def genomeSize_auto_or_not(given_size): return given_size -def addUniqueLibraryID(library): - string2Add=library + "_1" -def to_be_smrtTrimmed(userAnswer): - if userAnswer == 'True': - string2Add="smrtTrimmed" - elif userAnswer == 'False': - string2Add="notsmrtTrimmed" + + # def to_be_smrtTrimmed(userAnswer): + # if userAnswer == 'True': + # string2Add="smrtTrimmed" + # elif userAnswer == 'False': + # string2Add="notsmrtTrimmed" samples = pd.read_csv(config['samplesTSV'], dtype=str, index_col=False, delim_whitespace=True, skip_blank_lines=True) if set(['sample', 'Library_R1', 'Library_R2', 'meryl_kmer_size', 'trim10X', 'trimAdapters', 'fastQC']).issubset(samples.columns): diff --git a/envs/AUXILIARY_PYTHON_SCRIPTS.yaml b/envs/AUXILIARY_PYTHON_SCRIPTS.yaml index fb91762..06228f8 100644 --- a/envs/AUXILIARY_PYTHON_SCRIPTS.yaml +++ b/envs/AUXILIARY_PYTHON_SCRIPTS.yaml @@ -11,3 +11,4 @@ dependencies: - pandas - numpy - ghostscript + - python=3.9.* diff --git a/envs/UNZIP_and_QC.yaml b/envs/UNZIP_and_QC.yaml index e50ba80..34121fd 100644 --- a/envs/UNZIP_and_QC.yaml +++ b/envs/UNZIP_and_QC.yaml @@ -1,11 +1,12 @@ channels: - anaconda - - bioconda - conda-forge + - bioconda dependencies: - - pigz=2.4 - - trim-galore=0.6.6 - - pandoc=2.11 + - openssl==3.0.5 + - python=3.10.5=ha86cf86_0_cpython + - pigz=2.6 + - trim-galore=0.6.7 + - pandoc=2.11.4 - multiqc=1.9 - - python=3.8.5 - trimmomatic=0.39 diff --git a/rules/evaluate.smk b/rules/evaluate.smk index 7e81eff..c336a20 100644 --- a/rules/evaluate.smk +++ b/rules/evaluate.smk @@ -31,7 +31,7 @@ rule unzipFastq_R1_HiC: output: temp(os.path.join(config['Results'], "1_evaluation/{asmID}/HiC_MAPS/{asmID}.HiC.R1.fastq")), log: - os.path.join(config['Results'], "1_evaluation/{asmID}/logs/pigzUnzip..HiC.R1.{asmID}.log") + os.path.join(config['Results'], "1_evaluation/{asmID}/logs/pigzUnzip.HiC.R1.{asmID}.log") conda: os.path.join(workflow.basedir, "envs/UNZIP_and_QC.yaml") threads: @@ -56,7 +56,7 @@ rule symlink_UnzippedFastq_R1_HiC: None shell: """ - ln -s {input} {output} + ln -sf {input} {output} """ @@ -94,7 +94,7 @@ rule symlink_UnzippedFastq_R2_HiC: None shell: """ - ln -s {input} {output} + ln -sf {input} {output} """ @@ -334,7 +334,7 @@ rule symlink_UnzippedFasta_PRI: None shell: """ - ln -s {input} {output} + ln -fs {input} {output} """ ################ @@ -350,7 +350,7 @@ rule unzipFasta_ALT: log: os.path.join(config['Results'], "1_evaluation/{asmID}/logs/pigzUnzip.ALT.{asmID}.log") conda: - os.path.join(workflow.basedir, "envs/pigz.yaml") + os.path.join(workflow.basedir, "envs/UNZIP_and_QC.yaml") threads: resource['unzipFasta_ALT']['threads'] resources: @@ -431,7 +431,7 @@ rule merqury: os.path.join(workflow.basedir, "envs/MERYL_MERQURY.yaml") shell: """ - ln -s {input.merylDB_provided} {params.symlink_merylDB} + ln -fs {input.merylDB_provided} {params.symlink_merylDB} cd {params.outPath} export OMP_NUM_THREADS={threads} (merqury.sh {params.symlink_merylDB} {input.assemblyPRI} {input.assemblyALT} {params.outFile}) &> {log} -- GitLab